Method of identification of genotype and subtype of hepatitis c virus on a biological microchip

ABSTRACT

The invention relates to molecular biology, virology and medicine and provides a method for identifying a genotype and a subtype of Hepatitis C virus (HCV) on the basis of the analysis of an HCV genome NS5B region using a differentiating biochip. The method of the present invention is based on a two-step PCR, with a fluorescent labeled, preferably single-stranded, NS5B region fragment obtaining, followed by the hybridization of this fragment on a biochip comprising a set of specific discriminating oligonucleotides. HCV genotype and subtype identification is carried out by defining the specific sequences of the segments of the NS5B region fragment. The invention allows one to conduct an assay precisely from a clinical specimen, to determine 6 genotypes and 36 subtypes of hepatitis C virus, including the most virulent and drug resistant forms, and to reduce the cost of assay. Also, the invention deals with a biochip, a design method and a set of oligonucleotide probes usable under the implementation of the method.

TECHNICAL FIELD

The present invention relates to molecular biology, virology and medicine and deals with a method of identification of a genotype and subtype of Hepatitis C virus (HCV) on the basis of the analysis of an HCV genome NS5B region using a differentiating biochip.

BACKGROUND ART

HCV is related to the Flaviviridae RNA-containing virus family and causes an infectious process with the most frequent complication of cirrhosis and hepatocarcinoma (Surveillance Hepatitis. CDC Report No 61; Younossi Z, Kallman J, Kincaid J. The effects of HCV infection and management on health-related quality of life. Hepatology. 2007 March; 45(3): 806-16). More than 170 million people on the planet are afflicted by this disease, and the number of the affected is on the increase. There are about 1.5 million hepatocarcinoma cases world-wide caused by HCV infection. Said disease-related loss in the USA alone are 200 mln $—an yearly estimate.

A contemporary wide-spread trend in HCV treatment is the use of combination therapy comprising co-injection of megadoses of interferon with a cocktail containing both common antiviral preparations and one or two inhibitors of HCV replication (specific protease-helicase and/or RNA-polymerase inhibitors) (Toniutto P, Fabris C, Bitetto D, Fornasiere E, Rapetti R, Pirisi M. Valopicitabine dihydrochloride; a specific polymerase inhibitor of Hepatitis C virus. Curr Opin Investig Drugs. 2007 February; 8(2):150-8; Johnson C L, Owen D M, Gale M Jr. Functional and therapeutic analysis of Hepatitis C virus NS3. 4A protease control of antiviral immune defense. J Biol Chem. 2007 April; 282(14): 10792-803). These cocktails increase the percentage of recovery, however inevitably leading to the formation of adaptive, inhibitor-resistant HCV mutants.

The identification of a genotype and subtype of an HCV specimen is of substantive importance for the purpose of detecting treatment response, evaluating duration and efficacy of antiviral therapy and establishing a route of virus propagation.

To define HCV genotypes and subtypes, methods currently used are as follows:

I. Direct determination of a nucleotide sequence (Sequencing) of an HCV 5′-noncoding region with the subsequent analysis of a determined sequence as compared to the available database to determine the attribution of studied HCV sample to a certain genotype and subtype (kit ‘THUGENE HCV 5′ NC' (Bayer HealthCare LLC, USA)):

Jeffrey J. Germer, David W. Majewski, Michael Rosser, Amber Thompson, P. Shawn Mitchell, Thomas F. Smith, Slava Elagin, and Joseph D.C. Yao. 2003. Evaluation of the ‘THUGENE HCV S’ NC Genotyping Kit with the New GeneLibrarian Module 3.1.2 for Genotyping of Hepatitis C virus from Clinical Specimens. J Clin Microbiol, Vol. 41, No. 10, p. 4855-4857.

II. Line Probe assay (LiPA):

Zheng X, Pang M, Chan A, Roberto A, Warner D, Yen-Lieberman B. 2003. Direct comparison of Hepatitis C virus genotypes tested by INNO-LiPA HCV II and TRUGENE HCV genotyping methods. J Clin Virol. October; 28(2):214-6;

Verbeeck J, Maes P, Wollants E, Van der Merwe S, Song E, Nevens F, Van Ranst M. 2005. Use of a commercially available line probe assay for genotyping of Hepatitis C virus 5a strains. J Clin Microbiol. December; 43(12): 61 17-9.

III. Method of extension of genotype-specific primer (Primer-specific extension analysis):

Antonishyn N A, Ast V M, McDonald R R, Chaudhary R K, Lin L, Andonov A P, Horsman G B. 2005. Rapid genotyping of Hepatitis C virus by primer-specific extension analysis. J Clim Microbiol. October; 43(10): 5158-63.

IV. Mass-spectrometry methods (Matrix-assisted laser desorption ionization-time of flight (MALDI mass spectrometry)):

Ilina E N, Malakhova M V, Generozov E V, Nikolaev E N, Govorun V M. 2005. Matrix-assisted laser desorption ionization-time of flight (mass spectrometry) for Hepatitis C virus genotyping. J Clin Microbiol. June 1 43(6):2810-5.

V. Methods of enzyme immunoassay (Serotyping of Hepatitis C virus):

Elsawy E M, Sobh M A, El-Chenawi F A, Hassan I M, Shehab El-Din A B, Ghoneim M A 2005. Serotyping of Hepatitis C virus in hemodialysis patients: comparison with a standardized genotyping assay Diagn Microbiol Infect Dis. February; 51(2): 91-4.

VI. Heteroduplex analysis using capillary electrophoresis (heteroduplex mobility analysis using temperature gradient capillary electrophoresis):

Margraf R L, Erali M, Liew M, Wittwer C T. 2004. Genotyping Hepatitis C virus by heteroduplex mobility analysis using temperature gradient capillary electrophoresis J Clin Microbiol. 2004 October; 42(10):4545-51.

VII. Method of invasive probes (Invader Assay):

Germer J J, Majewski D W, Yung B, Mitchell P S, Yao J D. 2006. Evaluation of the invader assay for genotyping Hepatitis C virus. J Clin Microbiol. February; 44(2): 318-23.

VIII. Method of nested PCR with subsequent specific-structural restriction (Nested restriction site-specific PCR):

Krekulova L, Rehak V; Wakil A E, Harris E, Riley L W. 2001. Nested restriction site-specific PCR to detect and type Hepatitis C virus (HCV): a rapid method to distinguish HCV subtype 1b from other genotypes. J Clin Microbiol. May; 39(5): 1774-80.

IX. High-performance liquid chromatography (denaturing high-performance liquid chromatography):

Liew M, Erali M, Page S, Hillyard D, Wittwer C. 2004 Hepatitis C genotyping by denaturing high-performance liquid chromatography. J Clin Microbiol. January; 42(1): 158-63.

X. Transcription mediated amplification in conjunction with probe method (transcription-mediated amplification in conjunction with the line probe assay):

Comanor L, Elkin C, Leung K, Krajden M, Kronquist K, Nicolas K, Horansky E, deMedina M, Kittichai P, Sablon E, Ziermann R, Sherlock C. 2003 Successful HCV genotyping of previously failed and low viral load specimens using an HCV RNA qualitative assay based on transcription-mediated amplification in conjunction with the line probe assay. J Clin Virol. September; 28(1): 14-26.

XI. Real-time PCR followed by melting curve analysis (Melting curve analysis):

Doris M. Haverstick, Grant C. Bullock, and David E. Bruns. 2004. Genotyping of Hepatitis C virus by Melting Curve Analysis: Analytical Characteristics and Performance, Clinical Chemistry 50, No. 12, p. 2405-2407.

XII. Dirfect determination of a nucleotide sequence (Sequencing) of an HCV NS5B region followed by the constructing a phylogenetic tree and defining a genotype and subtype of the specimen assayed, on the basis of localization of the sequence analyzed in one of the clusters of the tree derived (NS5B sequencing followed by phylogenetic analysis):

K. Sandres-Saune, P.Deny, C. Pasquier, V. Thibaut, G. Duverlie, J. Izopet. 2003. Determining hepatitis C genotype by analyzing the sequence of the NS5B region. Journal of Virological Methods Vol. 109 pp 187-193;

Laperche S, Lunel F, Izopet J, Alain S, Deny P, Duverlie G, Gaudy C, Pawlotsky J M, Plantier J C, Pozzetto B, Thibault V, Tosetti F, Lefrere J J. 2005. Comparison of Hepatitis C virus NS5B and 5′ noncoding gene sequencing methods in a multicenter study. J. Clin Microbiol. February; 43(2): 733-9;

Hnatyszyn, J., Beld M., Gualbertus Hubertus M., Guettouche T., Gouw R., Van Der Meer, C., Beatrijs Maria. (Bayer Healthcare LLC). Methods and reagents for genotyping HCV. WO/2007/076493. International Application No PCT/US2006/062582. Publication Date: May 7, 2007.

Methods (I-IV, VI-XI) are based on the analysis of genotype—and subtype specific sequences of an HCV 5′-noncoding region (5′ NC). The analysis of the 5′ NC region makes it possible to clearly identify all the six HCV genotypes, albeit showing low efficiency (less than 70%) with reference to differentiation of subtypes belonging to genotype 1, specifically a subtype lb that is most virulent and resistant to ribavirin/interferon treatment (K. Sandres-Saune, P. Deny, C. Pasquier, V. Thibaut, G. Duverlie, J. Izopet. 2003. Determining hepatitis C genotype by analyzing the sequence of the NS5B region. Journal of Virological Methods Vol. 109 pp 187-193; Laperche S, Lunel F, Izopet J. Alain S, Deny P, Duverlie G, Gaudy C, Pawlotsky J M, Plantier J C, Pozzetto B, Thibault V, Tosetti F, Lefrere J J. 2005. Comparison of Hepatitis C virus NS5B and 5′ noncoding gene sequencing methods in a multicenter study. J Clin Microbiol. February; 43(2): 733-9; Cantaloube J F, Laperche S, Gallian P, Bouchardeau F, de Lamballerie X, de Micco P. Analysis of the 5′ noncoding region versus the NS5B region in genotyping Hepatitis C virus isolates from blood donors in France. J Clin Microbiol. 2006 June; 44(6):2051-6; Murphy D G, Villems B, Deschenes M, Hilzenrat N, Mousseau R, Sabbah S. 2007. Use of Sequence Analysis of the NS5B Region for Routine Genotyping of Hepatitis C virus with Reference to C/E1 and 5′UTR Sequences. J Clin Microbiol. February. 7).

At present only the analysis of a NS5B region permits identifying a subtype 1b with the specificity approaching 100%. Moreover, the investigation of sequences of the given region enables detection of a number of subtypes much greater than those in the analysis of the 5′ NC sequences (Thomas F, Nicot F, Sandres-Saune K, Dubois M, Legrand-Abravanel F, Alric L, Peron J M, Pasquier C, Izopet J. 2007. Genetic diversity of HCV genotype 2 strains in south western France. J Med Viol. January; 79(1): 26:34; Nicot F, Legrand-Abravanel F, Sandres-Saune K, Boulestin A, Dubois M, Alric L, Vinel JP, Pasquier C, Izopet J. 2005. Heterogeneity of Hepatitis C virus genotype 4 strains circulating in south-western France. J Gen Virol January; 86(Pt 1): 107-14).

Thus, the analysis of NS5B region sequence is now necessary for the identification of the genotype and subtype of an HCV specimen for the purpose of detecting a treatment response, evaluating duration and efficiency of antiviral therapy, establishing an infection route (Laperche S, Saune K, Deny P, Duverlie G, Alan S, Chaix M L, Gaudy C, Lunel F, Pawlotsky J M, Payan C, Pozzetto B, Tamalet C, Thibault V, Vallet S, Bouchardeau F, Izopet J, Lefrere J J. 2006. Unique NS5B Hepatitis C virus gene sequence consensus database is essential for standardization of genotype determinations in multicenter epidemiological studies. J Clin Microbiol February; 44(2):614-6; Kuiken C, Yusim K, Boykin L, Richardson R. 2005. The Los Alamos hepatitis C sequence database. Bioinformatics February 1; 21(3):379-84).

A method for sequencing an HCV NS5B region followed by a phylogenetic assay (X11) calls for amplification and sequencing reactions, a further purification of reaction products subsequent to each of the above-mentioned steps and the following automatic sequencer analysis. More, the following analysis of chromatograms, constructing the multiple alignment and building phylogenetic trees exact the highest requirements for the skill of laboratory personnel, a factor that is a bar to the comprehensive use of the given approach for the analysis of a current of clinical specimens in the conditions of an ordinary diagnostic laboratory.

A method for detecting serotypes through the use of variants of an enzyme immunoassay (V) permits indentifying only a restricted number of genotypes and subtypes (1a, 1b, 2a, 2b, 3a, and 4a) and calls for the presence of highly purified monoclonal antibodies for each and every serotype.

Likewise, above-listed methods of identification of genotypes and subtypes have the following drawbacks:

-   -   commercial kit INNO-LiPA (II) and its use in conjunction with         transcription-mediated amplification (X) is distinguished for         high cost and identifies a limited number of subtypes;     -   method based on the use of genotype-specific primers (III)         requires independent reactions by the number of genotypes (i.e.         no less than 6) to detect one genotype only;     -   PCR-heteroduplex analysis using capillary electrophoresis (VI)         and a method of nested PCR with subsequent specific-structural         restriction (VIII) are much labour- and time-consuming and         require standards for each genotype and/or subtype to be         determined;     -   method of invasive probes (VII) identifies only a genotype and         does not applicable for subtype determination, which is a         serious restriction for using same in clinical practice where it         is necessary to detect HCV drug-resistant varieties (at least 1b         and 4d) to evaluate the efficiency and duration of therapy;     -   methods of mass spectrometry (IV) and HPLC (IX) call for         availability of expensive equipment, additional steps for         preparing a specimen for assay and identify the limited number         of subtypes;     -   Real-time PCR (XI) detects the presence only of the most         wide-spread genotypes and subtypes and is very expensive for         routine analysis.

It is hence only logical to see that in the present field there is an urgent need of developing a method for identifying an HCV genotype and subtype that can be used to advantage against a background of solutions known from state of the art and is distinguished for the simplicity of conduct of an analysis, high specificity and information content with respect to the number of identifiable genotypes and subtypes and also low cost.

DISCLOSURE OF INVENTION

As a result of comprehensive research, the authors of the present invention have discovered that the task of working out a method for the identification of an HCV genotype and subtype can successfully be solved through the use of biological chips (microchips) for the analysis of an HCV genome NS5B region.

A method for the identification of a genotype and a subtype of Hepatitis C virus (HCV) on the basis of the analysis of an HCV geriome NS5B region on biochips is advantageously distinguished from methods known from state of the art adapted to detect all six genotypes (1-6) and 36 subtypes of Hepatitis C virus (la-le, 2a, 2b, 2c, 2d, 2i, 2j, 2k, 2l, 2m, 3a, 3b, 3k, 4a, 4c, 4d, 4f, 4h, 4i, 4k, 4n, 4o, 4p, 4r, 4t, 5a, 6a, 6b, 6d, 6g, 6h, 6k) in clinical specimens showing a specificity approximating 100% due to the analysis of the NS5B region sequence; and also low cost and little time required for obtaining results. The method does not call for expensive equipment and highly skilled personnel. Data provided by a method of hybridization on the biochips can be used for evaluating and predicting severity of a disease (acute/chronic cirrhosis, a likelihood of liver cancer development), determining a therapeutic dosage for medicaments and duration of a course of therapy as well as for epidemiological genotyping.

In its first aspect, the present invention provides for a method of identification of an HCV genotype and subtype on the basis of the analysis of an HCV genome NS5B region using an oligonucleotide biochip. The method of the present invention is based on a two-stage PCR for obtaining a fluorescent labeled, predominately single-stranded, fragment of the NS5B region followed by hybridization of this fragment on the biochip comprising a set of specific discriminating oligonucleotides complementary to the genotype- and subtype-sequences of NS5B region. The method includes the following steps:

(a) reverse transcription combined with PCR (RT-PCR) using a viral RNA as a template and a first pair of primers specific for an NS5B region fragment;

(b)—asymmetric amplification of the NS5B region fragment using as a template the RT-PCR product produced in step (a), a second pair of specific primers and a mixture of four deoxynucleoside triphosphates, wherein one of the said four deoxynucleoside triphosphates is fluorescent labeled, as a substrate, to provide substantially a single-stranded fluorescent labeled fragment;

(c)—providing a biochip for the identification of an HCV genotype and subtype representing a support comprising a set of discrete elements, with a unique oligonucleotide probe immobilized in each of them, having a sequence complementary to the sequence of a single-stranded fragment obtained in step (b) and selected from the group comprising:

a) corresponding NS5B region fragment sequences specific for each of the HCV genotypes (genotype-specific); and b) corresponding NS5B region fragment sequences specific for each of the HCV subtypes (subtype-specific);

(d)—hybridization an amplified labeled product from step (b) on a biochip with the formation of duplexes with immobilized probes in conditions providing for a single-nucleotide resolution between the hybridization perfect and imperfect duplexes;

(d)—registration and interpretation of hybridization results.

In one of its embodiments, a method is characterized in that in step (a) a first pair of specific primers is used whose sequences are set forth in SEQ ID NO: 121 and 122.

In another embodiment, a method is characterized in that in step (b) a second pair of specific primers is used whose sequences are set forth in SEQ ID NO: 121 and 123.

In its further embodiment, a method is characterized in that in step (b) one of the primers of the second pair is used in at least tenfold molar excess relative to a second primer.

In its further embodiment, a method is characterized in that in step (b) the fluorescent labeled deoxynucleoside triphosphate used corresponds to the fluorescent labeled deoxyuridine triphosphate.

In its still further embodiment, a Method is characterized in that the biochip is a hydrogel elements-based biochip obtained by the method of chemically or photoinduced copolymerization.

In one more embodiment thereof, a method is characterized in that a biochip comprises a set of immobilized oligonucleotides whose sequences are set forth in SEQ ID NO: 1-120.

According to another embodiment, a method is characterized in that registration of the results of step (d) is performed through the use of a portable analyzer of fluorescence and software, which permits using the software-based processing of signal intensities with the subsequent interpretation of results.

According to still another embodiment, a method is characterized in that interpretation of the registered results of step (d) is performed in two steps: in a first step, signals are analyzed in biochip elements comprising oligonucleotide probes specific for HCV genotypes thereby to identify the genotype of a specimen; analyzed are in case of a genotype being identified in a second step, only biochip elements comprising oligonucleotide probes specific for the subtypes of an identifiable genotype, regardless of the presence of signals in the elements comprising probes specific for the subtypes of other genotypes.

And last but not least, according to yet another embodiment, a method further comprises evaluating and predicting severity of a disease (acute/chronic cirrhosis, a likelihood of liver cancer development), determining a therapeutic dosage of medicaments and duration of therapy and/or epidemiological genotyping on the basis of interpretation of hybridization results.

In its following aspect, the present invention relates to a biochip for the identification of an HCV genotype and subtype, on the basis of NS5B region analysis that represents a support comprising a set of discrete elements, with a unique oligonucleotide probe immobilized in each of them, and the probe sequences are set forth in SEQ ID NO: 1-120.

In another embodiment of the given aspect of the present invention, a biochip is characterized in that it represents a biochip based on hydrogel elements that is obtained by a method of chemically or photoinduced copolymerization.

The following aspect of the present invention is a set of oligonucleotide probes for obtaining a biochip to indentify an HCV genotype and subtype on the basis of NS5B region analysis having the sequences of SEQ ID NO: 1-120.

And last but not least still another aspect of the present invention is a method for designing a set of oligonucleotide probes usable for constructing a biochip of the type used for identifying an HCV genotype and subtype on the basis of analysis of an NS5B region that provides for a separate selection of several discriminating probes for each and every genotype and subtype whose sequences are complementary to the sequences of different segments of an NS5B region fragment as assayed.

Other aspects of the present invention will become clear from the accompanying figures, the claims and a detailed specification.

BRIEF DESCRIPTION OF DRAWINGS

To gain a better insight into a concept of invention, as being claimed and as set forth in the application, and to demonstrate its characteristic features and advantages there is given a detailed description of invention with reference to the accompanying drawings illustrating a specific embodiment thereof, in which:

FIG. 1—schematic diagram of the analysis of an HCV NS5B region for identifying an HCV genotype and subtype on a biological microchip.

FIG. 2—diagram of a selection of oligonucleotides for the identification of genotypes and subtypes on the basis of the analysis of an HCV genome NS5B region fragment.

FIG. 3—diagram of biochip structure.

FIG. 4A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 1, subtype 1a.

FIG. 4B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 1, a subtype 1a.

FIG. 5A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 1, subtype 1b.

FIG. 5B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 1, subtype 1b.

FIG. 6A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 1, subtype 1e.

FIG. 6B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 1, subtype 1e.

FIG. 7A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 2, subtype 2a.

FIG. 7B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 2, subtype 2a.

FIG. 8A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 2, subtype 2i.

FIG. 8B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 2, subtype 2i.

FIG. 9A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 3, subtype 3a.

FIG. 9B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 3, subtype 3a.

FIG. 10A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 4, subtype 4a.

FIG. 10B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 4, subtype 4a.

FIG. 11A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 4, subtype 4d.

FIG. 11B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 4, subtype 4d.

FIG. 12A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 5, subtype 5a.

FIG. 12B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 5, subtype 5a.

FIG. 13A—a fluorescent hybridization pattern obtained on a biochip as a result of analysis of an HCV specimen having a genotype 6.

FIG. 13B—distribution of normalized signals of biochip elements obtained as the result of the analysis of an HCV specimen having a genotype 6.

DESCRIPTION OF EMBODIMENTS

The object of the present invention is to develop a method of identifying an HCV genotype and subtype, on the basis of the analysis of NS5B region using biological microchip.

The method envisages the following steps: a reverse transcription procedure combined with a polymerase chain reaction (RT-PCR) for the amplification of NS5B region fragment with the use of viral RNA isolated from clinical sample such as blood, plasma or liver biopsy material, accumulation of single-stranded fluorescent labeled NS5B fragment with the use of cDNA fragment obtained on RT-PCR step. Also, the method as claimed provides for using an original oligonucleotide biochip with immobilized specific probes, procedures of hybridization, registration and interpretation of results.

The General Concept of Identification of Genotype and Subtype of HCV Specimen Using Biochip.

The analysis diagram of the NS5B region fragment for the identification of HCV genotype and subtype using biochip is shown in FIG. 1.

Isolation of HCV RNA from a clinical specimen is carried out through the use of methods known in the given field (for example, Hourfar MK, Michelsen U, Schmidt M, Berger A, Seifried E, Roth W K. High-throughput purification of viral RNA based on novel aqueous chemistry for nucleic acid isolation. Clin Chem. 2005 July; 51(7): 1217-22) or any specialized commercially available kit of reagents for isolating RNA from blood, plasma or liver biopsy material, for example, QIAamp DSP Virus Kit (Cat No 60704, Qiagen, Germany), MagMAX™ AI/ND Viral RNA Isolation Kits (Cat. No AM1939, Ambion, USA) or “Kit of reagents for RNA isolation Cat. No 05-013, ZAO “DNA technology, Ltd, Russia).

Amplification of an HCV genome NS5B region fragment is carried out in a first step by reverse transcription reaction combined with PCR (RT-PCR). To perform RT-PCR various systems can be used, as shown and described, for example, in Casabianca A., Orlandi C., Fraternale A., Magnani M. A new one-step RT-PCR method for virus quantitation in murine AIDS. 2003 Journal of Virological Methods Vol 110(1), pp. 81-90, and commercially produced kits, e.g., OneStep RT-PCR Kit (Cat. No 210210, Qiagen, Germany), Accuscript® High-Fidelity RT-PCR Kit (Cat. No 600180, Stratagene, USA) etc.

Primers for performing a first amplification are selected in such a way as to flank the most polymorphic fragment of an NS5B region that allows to differentiate the existing HCV genotypes and subtypes. The NS5B region fragment being amplified is preferred to include HCV genome positions 8256 to 8645 according to Choo, Q. L., K. H. Richman, J. H. Han, K. Berger, C. Lee, C. Dong, C. Gallegos, D. Coit, R. Medina-Selby, P. J. Barr, et al. 1991. Genetic organization and diversity of the Hepatitis C virus. Proc. Natl. Acad. Sci. USA 88: 2451-2455.

Primer sequences are selected in such a way as to perform the effective RNA amplification of the analyzed NS5B region fragment, of any HCV genotype and, accordingly, subtype. For this purpose, the multiple sequence alignment may be constructed using available databases of NS5B region sequences, such as http://www.ncbi.nlm.nih.gov/Genbank/index.html and http://hcv.lani.gov/content/hcv-db. The next step includes the location of the most conservative segments within the analyzed fragment of NS5B region for all HCV genotypes and selection of primers specific to segments concerned. Using the specialized software, for example, Oligo v. 6.3 (Molecular Biology Insights Inc., USA) or Fast PCR (http://www.biocenter.helsinki.fi/bi/Programs/fastper.htm) or other commercially available programs or programs free accessible over a world wide web network, melting temperatures of primers are calculated and the lengths of primers are varied, thus providing for a spread of the annealing temperatures of the primers inside a pair of not greater than 3-4° C. Also, the sequences are to be avoided which are able to form secondary structures of a hairpin loop type with high melting temperatures. Each and every selected primer should show a unique specificity to the analyzed NS5B region fragment. The specificity of primers is verified with the help of software using a search in the bases of nucleotide sequences by the BLAST algorithm (www.ncbi.nlm.nih.gov/BLAST/). In particular, the sequences, capable of the efficient hybridization (annealing) with the human genome sequences, should be avoided.

In a second step, a single-stranded fluorescent labeled product is predominantly obtained by an asymmetric PCR using with the use of deoxynucleoside triphosphates mix as the substrate wherein one of said deoxynucleoside triphosphates is fluorescent labeled. Generally, the deoxynucleoside triphosphates mix consists of dATP, dGTP, dCTP

dTTP, and the latter can be replaced with dUTP or a mixture of dTTP/dUTP in any molar proportion. Any one of said deoxynucleoside triphosphates may be fluorescent labeled. Use of a fluorescent labeled deoxyuridine triphosphate is most preferable, which, on the one hand, necessitates the efficient incorporation of the present substrate in the newly synthesized DNA strand during PCR. On the other hand, the application of dUTP-fluorescent labeled conjugates makes it possible to prevent cross-contamination using uracil-DNA-glycosylase enzyme. The latter condition is important for the routine analyses in the clinical laboratory.

The fluorescent dye used can be represented by any fluorescent dye which may chemically be included in the deoxynucleoside triphosphate molecule in such a way as the final conjugate does not hamper the nucleic acids amplification and the subsequent hybridization of the polynucleotide molecule comprising such fluorescent labeled nucleotide residues with-immobilized oligonucleotide probes. In the case of a fluorescent labeled deoxyuridine triphosphate, for example, the fluorescent dye can be attached at the 5′-terminal of a dUTP aminoallyl derivative. Examples of such dyes are well known to a person skilled in the art and include fluorescein (TAMRA®, ROX®, JOE®), rhodamine (Texas Red®), polymethine (Cy3®, Cy5®, Cy5.5®, Cy7®) dyes (Ranasinghe R and Brown T). Fluorescence based strategies for genetic analysis. Chem. Commun, 2005, 5487-5502). The fluorescent dyes are commercially available, particularly from the Molecular probes company, USA. The dyes whose excitation spectrum is within a long-wave(red) region are most preferable, which permits using inexpensive semiconductor laser as exciting radiation sources for fluorescence excitation.

Fluorescent labeled deoxynucleoside triphosphates can be obtained in laboratory conditions using known methods, such as, for example (Kuwahara M, Nagashima J, Hasegawa M, Tamura T, Kitagata R, Hanawa K, Hososhima S, Kasamatsu T, Ozaki H, Sawai H. Systematic characterization of 2′-deoxynucleoside-5′-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA. Nucleic Acids Res. 2006 34(19): 5383-94 and are also commercially available, for example, CyDye Fluorescent Nucleotides (Cat. No PA55021, PA55032, PA55026, GE Healthcare, USA).

Primers for the second step of amplification are selected with the requirements set forth above, with the only difference that at least one of the primers is' selected inside a PCR fragment from the first step, to enhance reaction specificity. It is hence only logical to see that the resulted PCR fragment will be a product of semi-nested or nested amplification reaction. The length of a second-step amplified fragment is not especially restricted until this enables the efficient hybridization of a fragment with biochip-immobilized probes. In case of biochip with hydrogel elements, the primers for the second amplification step are selected such that the length of an amplified fragment should not exceed 800 nucleotides. The greater length of a PCR product from the second step makes difficult the efficient diffusion of a PCR product as assayed in biochip gel elements during the hybridization, which may result in reducing the number of hybridization duplexes and, consequently, a fluorescent signal fall. On primers design, account should be taken of the fact that single-stranded fluorescent labeled fragment yielded from a second PCR step should be complementary to oligonucleotides immobilized on the biochip. Therefore in each and every pair, the primer added in an excessive amount (”leader primer“) is selected from a chain whose sequence is complementary to the sequences of the biochip-immobilized oligonucleotides. That is, should immobilization oligonucleotides be selected from a sense chain, for hybridization duplexes to be formed in biochip elements, there is a need for the primary amplification of an antisense chain and the “leader primer” is thus selected from the chain complementary to a gene sequence (antisense chain), and vice versa.

To provide predominantly a single-chain fluorescent labeled product, a leader primer is added in an excessive molar amount in relation to a second primer. Preferably the molar excess is at least tenfold.

On selection of discriminating oligonucleotides for immobilization on a biochip to take account of the size and complexity of a sequence as assayed and, in particular, the presence of replicas and extended homopolymeric sequences, there is determined a length of the discriminating oligonucleotides that provides their specificity relative to the sequence as assayed.

Selection of discriminating oligonucleotides for genotypes and subtypes is carried out in the following mariner. Using constructed multiple alignment of NS5B region sequences, the special consensus sequence is generated for each genotype on whose basis are selected unique probes permitting uniquely identifying each and every genotype. Owing to the high variability of an HCV genome, for enhancing the reliability of a method, several discriminating probes for each of the genotypes are selected, if possible, complementary to various segments of the NS5B region fragment as assayed. The consensus sequence is also generated for each subtype followed by the location of segments of the NS5B region fragment which enable to differentiate the maximum number of subtypes inside one genotype. The number of such segments should be enough for providing the reliable identification of each of the subtypes. On the basis of the sequences of the segments selected, probes are constructed for the identification of subtypes, and the sequence of one probe may conform to two or more subtypes simultaneously in the separate differentiating segment of the NS5B region fragment as assayed. The strategy of probes selection for biochip immobilization is schematically shown in FIG. 2.

Using the software, for example, Oligo v. 6.3 (Molecular Biology Insights Inc., USA), melting temperatures of oligonucleotides are calculated and the lengths of probes are varied thereby to provide for a variation of melting temperatures of the oligonucleotides ranging between 2 and 3° C. Oligonucleotides are avoided which are capable of forming secondary structures of a hairpin loop type with high melting temperatures.

Discriminating oligonucleotides are immobilized on a biochip support. The suitable support that might be used to produce the biochip are represented by an activated, say, aminated surface of glass slides (Adessi C., Matton G., Ayala G., Turcatti G., Mermod J., Mayer P., Kawashima E. Solid phase DNA amplification: characterization of primer attachment and amplification mechanisms Nucleic Acids Research. 2000. V.51. 28(20): E87), plastic wafers (Nikiforov T., Rendle R. Goelet P., Rogers Y., Kotewicz M., Anderson S., Trainor G., Knapp Michael R. Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Research. 1994. 22(20):4167-75), wafers with polymeric macroporous carriers. such as acrylamide (Timofeev E., Kochetkova S., Mirzabekov A., Florentiev V. Regioselective immobilization of short oligonucleotides to acrylic copolymer gels. Nucleic Acids Res. 1996 24 (16):3142-8, a cepharose (Margulies M, Egholm M, Altman W E, Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005 437(7057): 376-80) et al. Methods of immobilizing the oligonucleotides on substrates are well known in the given field and comprise:

-   -   chemosorption of oligonucleotides and DNA comprising a thiol         group on metals (Mirkin C. A., Letsinger R. L., Mucic R. C. and         Storhoff J. J. A DNA-based method for rationally assembling         nanoparticles into macroscopic materials. Nature. 1996 Aug. 15;         382(6592):607-9);     -   covalent binding of modified oligonucleotides with functional         groups of a surface based on the reactions of amide bond         formation (Healey B G, Matson R S, Walt D R. Fiberoptic DNA         sensor array capable of detecting point mutations. Anal Biochem.         1997 251(2): 270-9), ester bond formation (Ghosh S S, Musso G F.         Covalent attachment of oligonucleotides to solid supports.         Nucleic Acids Res. 1987 15(13):5353-72), carbamimidoyl function         (Matson R S, Rampal J, Pentoney S L, Anderson P D, Coassin P.         Biopolymer synthesis on polypropylene supports: oligonucleotide         arrays. Anal Biochem. 1995 Jan. 1; 224(1):110-6), to mention         only few;     -   photochemically, chemically and electrochemically induced         copolymerization of oligonucleotides carrying an unsaturated         group with monomers being the basis for a solid phase to be         formed (Vasiliskov A. V., Timofeev E. N., Surzhikov S. A.,         Drobyshev A. L., Shick V. V. and Mirzabekov A. D., Fabrication         of microarray of gel-immobilized compounds on a chip by         copolymerization. Biotechniques, 1999, 27, 592-606).

In a preferable embodiment of the present invention, use is made of a biochip based on hydrogel elements. Methods for producing such biochips comprise polymerizing amino-modified oligonucleotides to create a covalent bond with gel monomers in suitable conditions (pH, temperature, composition of polymers and so on) (Rubina A Y, Pan'kov S V, Dementieva E I et al. Hydrogel drop microchips with immobilized DNA: properties and methods for large-scale production. Anal Biochem 2004; 325: 92-106). Use of biochips comprising gel elements are most preferable, which are applied to a support dropwise with a dia. of 80 to 300 mcm at an interval of 150 to 500 mcm without using special devices—quartz masks, for example. The support used can be represented by a glass substrate (glass slides or cover glass) as well as more available materials, such as plastic materials. To immobilize the oligonucleotides into gel elements of biochip their copolymerization with main gel components is used. As result of this single-stage reaction the immobilized molecules are irreversibly attached in a covalent manner to some or other monomers of a growing polymeric chain and uniformly distributed within the entire volume of a gel with a high yield (about 50% for oligonucleotides) (Rubina A Y, Pan'kov S V, Dementieva E I et al. Hydrogel drop microchips with immobilized DNA: properties and methods for large-scale production. Anal Biochem 2004; 325: 92-106). The concentration of immobilized oligonucleotide probes can be judged by staining the gel elements of the biochip with a dye showing a low specificity to a DNA nucleotide sequence (A. L. Mikheikin, A. V. Choudinov, A. I. Yaroschuk, A. Yu. Roubina, S. V. Pan'kov, A. S. Krylov, A. S. Zasedatelev, A. D. Mirzabekov. The dye showing a low specificity to the DNA nucleodie sequence: use for evaluating the number of oligonucleotides immobilized in the elements of biological microchips. Molecular biology 2003; 37(6): 1061-70).

PCR-products from a second amplification step are hybridized on a biochip with immobilized differentiating oligonucleotides complementary to the consensus sequences of genotypes and subtypes of an NS5B region fragment. Hybridization is carried out in a solution containing a buffer component for maintaining a pH value, a salt for creating ionic strength and a chaotropic (hydrogen-bond destabilizing) agent in a hermetically sealed hybridization chamber at a temperature depending on the melting temperatures of immobilized discriminating oligonucleotides. The hydrogen-bond destabilizing agent that might be used can be represented by, for example, guanidine thiocyanate, urea or formamide. A choice of the most favourable hybridization temperature is made to take account of convenience of the practical use of a system. The discriminating oligonucleotides of the present invention have melting temperatures ranging between 42 and 44° C., which fact allows one to carry out hybridization at 37° C. using said chaotropic agent. The temperature of 37° C. is suitable in that a majority of clinical laboratories are equipped with thermostats maintaining this temperature.

The DNA fragment, as assayed, forms perfect hybridization duplexes only with adequate (fully complementary) oligonucleotides. With all the remaining oligonucleotides said DNA fragment provides an imperfect duplex. Said perfect and imperfect duplexes are discriminated by comparing the fluorescence intensities of biochip elements wherein the duplexes have formed. The signal strength in the element with the perfect hybridization duplex formed therein (I perf.) is higher than in the element where imperfect duplex (I imperf.) has been formed. Hybridization performed in the most favourable conditions (temperature, the concentration of a chaotropic (hydrogen—bond—destabilizing) agent and hybridization buffer ionic strength) provides a I_(perf.)/I_(imperf.)≧1.5 ratio between two elements comprising probes belonging to one group and differing by one nucleotide.

Registration of hybridization results on biochips can be performed with the aid of commercial scanning devices—analyzers of biochip fluorescence, for example, GenePix 4000B (Axon Instruments, USA) equipped with the adequate software for calculating the strength of fluorescent signals of the discrete elements of a biochip and their subsequent normalization for a background value, for example, ‘GenePix Pro’, ‘Acuity’ (Axon Instruments, USA).

Interpretation of hybridization results can be performed Visually through the correlation of the registered fluorescence pattern of a biochip and/or distribution of the signal strength of biochip elements thus obtained to the arrangement of specific discriminating probes in the biochip elements (cf. FIG. 3). Given the distributed signal strength in biochip elements, a maximum signal is detected from among the elements comprising genotype-specific oligonucleotides. A genotype can be identified by providing a biochip element having a maximum fluorescence intensity among the probe-containing elements to determine an HCV genotype. Identification of the subtype of an HCV specimen as assayed can be realized by determining the maximum signals in the elements containing subtype-specific oligonucleotides corresponding to the genotype, as determined, in case of the maximum signals being registered in at least two different elements which contain unique subtype-specific probes.

Interpretation of hybridization results on biochips is preferably performed in the following manner. First step: extraction of valid signals, more exactly the signals in elements, wherein perfect duplexes might be formed, for which purpose the normalized fluorescent strength signals of all biochip elements are classified as to increase and compared with an average signal (I_(ref)) in the elements devoid of any oligonucleotides. The valid signals are those exceeding I_(ref) at least 1.5 times. Second step: starting with an analysis of filtered valid signals G_(i) in the groups of elements containing genotype-specific oligonucleotides (i—genotype number). A maximum signal is extracted inside each group of elements G_(imax) and compared with each other. If the signal G_(imax) in one group exceeds the maximum signals in the remaining groups more than 1.5 times (a threshold value), a conclusion is drawn on a specimen, as assayed, belonging to the given genotype. If a ratio of signals among G_(inmax) does not exceed the threshold value, a conclusion is made on the impossibility to clearly identify a genotype and on the possible presence in the specimen, as assayed, of a mixture of two and more HCV variants with various genotypes. If the signals in genotype-specific-oligonucleotides-containing groups do not undergo primary filtration in relation to the I_(ref), a conclusion is drawn on low signal strength and the possible absence of an HCV RNA in the specimen as assayed.. And no subtype identification is performed whatever.

Thus, given the determined genotype on the basis of a signal G_(imax), value, a consideration is further given to only the groups of elements comprising oligonucleotides specific for subtypes relating to an identifiable genotype. In accordance with the proposed strategy of selecting probes for the identification of a subtype, the oligonucleotides are combined in groups according to the selected segments of an NS5B fragment as assayed that permits differentiating the maximum number of the subtypes. And the number of groups is varied from one to four in relation to the degree of homology of the consensus sequences of the NS5B fragment for various subtypes and is dictated by the need for a reliable differentiation of subtypes inside the genotype. On identification of the subtype first picked out are signals inside each group of the elements exceeding the remaining signals of this group at least 1.5 times. This signal is designated as S_(ixj) (i—genotype number, ‘x’—symbol of a subtype according to HCV subtype classification, j—group number). Should two or more elements in the group have signals differing from one another less than 1.5 times, then all such signals—S_(ixj), S_(ixj), to mention only few, are picked out. The result: a set of elements from various groups ix1, iy1, ix2, iz2, ix3, etc. whose signals exceed the rest of signals in their groups no less than 1.5 times. And if in the set so obtained are present at least two elements from various groups homologous to one subtype, for example, ix1 and ix3 or ix1 and ixy2, a conclusion is drawn on the assayed specimen belonging to the subtype ‘x’ of a genotype ‘i’. Should the elements of different groups in the set so obtained conform to different genotypes, for example, ix1, iy2, iz3 or ix1, iyz3, then the signals of the given elements are compared with each other. If the signal of a element conforming to the subtype ‘x’ of one group exceeds the signals of the elements of other groups 3 times or more, a conclusion is drawn on the assayed specimen belonging to the subtype ‘x’. If a ratio of signals S_(ix1)/S_(iy2) does not exceed 3, a conclusion is drawn on the fact that the subtype is not determined and possible is identity to the subtype ‘x’ or the subtype ‘y’. The same conclusion is drawn if the maximum signal in the group belongs to an element containing an oligonucleotide showing specificity to two subtypes, for example, ixy1, with valid signals absent in other groups of the elements. If the signals of subtype-specific-oligonucleotides-containing groups do not undergo primary filtration with respect to I_(ref), it is believed that the subtype of a specimen as assayed is not determined.

The evaluation of duration of antiviral therapy and prognosis can be made on the basis of data on genotype/subtype identification. Thus, in case of a genotype 1 being determined that elicits cirrhosis, chronic hepatitis and hepatocarcinoma, duration of pegylated interferon/ribavirin therapy is no less than 24 weeks for subtypes 1a, 1c, 1 d, 1e and in case of subtype 1b being detected that is interferon-resistant—no less than 48 weeks (Weck K. Molecular methods of hepatitis C genotyping. Expert Rev Mol Diagn. 2005 July; 5(4): 507-20).

The infection caused by HCV with a genotype 4 provides a clinical picture similar to virus genotype 1 infection (Legrand-Abravanel F, Nicot F, Boulestin A, Sandres-Sauné K, Vinel J P, Alric L, Izopet J. Pegylated interferon and ribavirin therapy for chronic Hepatitis C virus genotype 4 infection. J Med Virol. 2005 September; 77(1):66-9). And unlike the genotype 1, the genotype 4 is distinguished for splitting into a considerably greater number of subtypes (Nicot F, Legrand-Abravanel F, Sandres-Saune K, Boulestin A, Dubois M, Alric L, Vinel JP, Pasquier C, Izopet J. 2005. Heterogeneity of Hepatitis C virus genotype 4 strains circulating in south-western France. J Gen Virol January; 86(Pt 1): 107-14). The clinical significance of some of them, for example, 4a and 4d has already been established—4d is resistant to interferon and calls for a prolonged course of treatment (no less than 48 weeks) (Roulot D, Bourcier V, Grando V, Epidemiological characteristics and response to peginterferon plus ribavirin treatment of Hepatitis C virus genotype 4 infection (J Viral Hepat. 2007 July; 14(7): 460-7).

The subtypes of HCV genotypes 2 and 3 are responsive to therapy with drugs and lead to chronic disease in significantly lesser amount of cases. Duration of ribavirin/interferon therapy for HCV infected patients with the given genotypes is 6 to 12 weeks.

Apart from prognostic purposes and evaluation of duration of therapy, the definition of a genotype and subtype provides information in terms of etiology of infection. Subtypes 1a, 3a, 4a, 4d are most commonly associated with intravenous drug users, whereas a genotype 2 and a subtype 1 are linked with a blood transfusion transfer route (Simmonds P, Bukh J, Combet C. Consensus proposals for a unified system of nomenclature of Hepatitis C virus genotypes. Hepatology. 2005 October; 42(4): 962-73).

Lastly the results obtained by means of the method of the present invention can be made use of for epidemiological genotyping. Distribution of HCV genotypes and subtypes is varied in various geographic regions (Zein N N. Clinical significance of Hepatitis C virus genotypes. Clin Microbiol Rev. 2000 13(2):223-35). Some subtypes are universal, other circulate only within limited geographic zones. Subtype 1b prevails in the south of Europe, China, Japan and in Russia (50-80%). In the USA and countries of South America, in the north of West Europe, subtypes 1a and 1b are dominated, followed by genotypes 2 and 3. Genotype 4 prevails in North Africa and Central Africa, whereas in the south of the continent, a genotype 5 is predominant. Genotype 3 is met almost everywhere whose domain are Australia and South-East Asia. Genotype 6 is likewise widespread in South-East Asia and is predominant in Vietnam, a major type in Thailand, Indonesia.

The invention will now be exemplified to grasp a better idea of a concept of invention, as being claimed and as set forth in the application, but the illustrative examples shouldn't be considered restricting the present invention.

Examples Example 1 Biochip for Identifying HCV Genotype and Subtype on the Basis of NS5B Region Assay

1. Oligonucleotides for immobilization on a biochip and primers for amplification were synthesized on an automatic synthesizer—394 DNA/RNA synthesizer (Applied Biosystems, USA) and contained a spacer with a free amino group 3′-Amino-Modifier C7 CPG 500 (Glen Research, USA) for the following immobilization to a gel. Biochips were produced according to the procedure thus far described ((Rubina A Y, Pan'kov S V, Dementieva E I et al. Hydrogel drop microchips with immobilized DNA: properties and methods for large-scale production. Anal Biochem 2004; 325: 92-106). The biochips contained hemispherical elements, 100 mcm in dia., through a distance of 300 mcm. Uniformity of the application of elements and their dia. were assessed with the help of the software ‘Test-chip’ (Biochip-IMB, Russia). The qualitative control of microchips was made by measuring the concentrations of immobilized oligonucleotides. The biochips were stained with a fluorescent dye-ImD-310 (Biochip-IMB), the concentration of immobilized probes was assessed as described above (A. L. Mikheikin, A. V. Choudinov, A. I. Yaroschuk, A. Yu. Roubina, S. V. Pan'kov, A. S. Krylov, A. S. Zasedatelev, A. D. Mirzabekov. A dye showing a low specificity to a DNA nucleotide sequence: use for the evaluation of the number of nucleotides immobilized in biological microchip elements. Molecular biology 2003; 37(6): 1061-70).

Biochip Structure

A biochip comprises 120 immobilized oligonucleotides whose list is presented in Table I, four marker points (M) for accurate positioning (image acquisition), performed by a software, and four elements of an empty gel (0) necessary for computing a reference (background) value of fluorescence intensity I_(ref). Arrangement of oligonucleotides immobilized on a microchip is shown in FIG. 3.

In two top rows, oligonucleotides are immobilized with a ‘G’ index permitting identifying a HCV genotype. A biochip identifies all six. HCV genotypes.

Immobilized below are oligonucleotides allowing for identifying subtypes:

-   inside a genotype 1: 1a, 1b, 1c, 1d, 1e. For the reliable     identification of each and every subtype of the genotype 1 four     groups of oligonucleotides have been constructed, each group is     conforming to a separate segment within an NS5B region fragment as     assayed: -   inside a genotype 2: 2a, 2b, 2c, 2d, 2i, 2j, 2k, 2l, 2m. For the     reliable identification of each and every subtype of the genotype 2     three groups of oligonucleotides have been constructed, each group     is conforming to a separate segment within an NS5B region fragment     as assayed; -   inside a genotype 3: 3a, 3b, 3k. For the reliable identification of     each-and every subtype of the genotype 3 three groups of     oligonucleotides have been constructed, each group is conforming to     a separate segment within an NS5B region fragment as assayed; -   inside a genotype 4: 4a, 4c, 4d, 4f, 4h, 4i, 4k, 4n, 4o, 4p, 4r, 4t.     For reliable identification of each and every subtype of the     genotype 4 four groups of oligonucleotides have been constructed,     each group is conforming to a separate segment within an NS5B region     fragment as assayed; -   inside a genotype 5: 5a. The genotype 5 is a single subtype 5a, with     the genotype-identifying probes thus identifying the subtype 5a; -   inside a genotype 6: 6a, 6b, 6d, 6g, 6h, 6k. For the reliable     identification of each and every subtype of the genotype 6 two     groups of oligonucleotides have been constructed, each group is     conforming to a separate segment inside an NS5B region fragment as     assayed.

TABLE 1 List of oligonucleotides immobilized on biochip Position of oligonucleotide in NS5B region SEQ ID sequence (Acc. NO: Oligonucleotide* Genotype Subtype Group Sequence 5′→3′** No M62321) 1 G1-1 1 — G1 GCC TGT CGA GCY GC 904-917 2 G1-2 1 — G1 GCC TGT CGA GCY GCR 904-918 3 G1-3 1 — G1 GCC TGT MGA GCY GCR 904-918 4 G1-4 1 — G1 GGC TTT AYR TCG GGG G 776-791 5 G2-1 2 — G2 TAC AGG CGY TGY CGC 826-840 6 G2-2 2 — G2 CTG CGG NTA CAG GCG TTG 819-836 7 G2-3 2 — G2 CTG CGG NTA CAG GCG YTG 819-836 8 G3-1 3 — G3 YCT TGT CTG CGG AGA Y 939-954 9 G3-2 3 — G3 GGC TTT ACT GCG GGG G 776-791 10 G4-1 4 — G4 CGA GGA RGA GGT CTA YCA GTG 705-725 11 G4-2 4 — G4 CGA GGA RGA GGT MTA YCA GTG 705-725 12 G4-3 4 — G4 GTG ACC TRG AGC CCG A 728-743 13 G5-1 5 — G5 GTG ACT TRC AGC CCG A 728-743 14 G5-2 5 — G5 GCA CGC TCC TGG TGT G 932-947 15 G6 6 — G6 TGA CAT GTT GGT CTG CG 933-949 16 1a11 1 1a 1 CAC TGA GAG CGA CAT CC 684-700 17 1ce1 1 1c/1e 1 CAC TGA GGC TGA TAT CCG 684-701 18 1a12 1 1a 1 YAT CCG TAC GGA GGA GG 696-712 19 1bd12 1 1b/1d 1 YAT CCG TGT TGA GGA GTC 696-713 20 1a2 1 1a 2 CAT CAA GTC CCT CAC YGA 756-773 21 1b2 1 1b 2 ATA ARG TCG CTC ACA GAG 757-774 22 1c2 I 1c 2 CCA TAA GGT CTC TCA CAG A 755-773 23 1d2 1 1d 2 ATA AAG TCG CTC ACC G 757-772 24 1e2 1 1e 3 ATC AAG TCY TTG ACT GAAA G 758-776 25 1a31 1 1a 3 AGG CCC GRG CAG C 893-905 26 1a32 1 1a 3 AGG CCC ARG CAG C 893-905 27 1b3 1 1b 3 GCC WCT GCR GCC TGT 895-909 28 1bd3 1 1b/1d 3 CCW CTG CGG CCT GT 896-909 29 1c3 1 1c 3 GCC AGT GCA GCC TGT 895-909 30 1e3 1 1e 3 CAA GGC CCT AGC AGC 891-905 31 1d3 1 1d 3 GCC ATR GCR GCC TG 895-908 32 1a4 1 1a 4 CTA YCG CAG GTG CCG 825-839 33 1b4 1 1b 4 GTT ATC GCC GGT GC 824-837 34 1c4 1 1c 4 GCT ATC GGC GAT GC 824-837 35 1d4 1 1d 4 GCT ACC GTC GGT GC 824-837 36 1e4 1 1e 4 TAT CGC AGA TGC CGT 826-840 37 2ad1 2 2a12d 1 CAG AAH TGA GGA GTC CATA 699-717 38 2b11 2 2b 1 ACG GAG AGG GAC ATA AG 685-701 39 2b12 2 2b 1 CAT AAG AAC AGA AGA ATC CA 696-715 40 2i1 2 2i 1 TCA CYG AAA GRG ACA TCA G 683-701 41 2cj1 2 2c/2j 1 YAG AAC CGA GGA GTC C 699-714 42 2k1 2 2k 1 ACG GAG AGR GAT ATC AGG 685-702 43 2l1 2 2l 1 ATA CGG ACA GAA GAA TCC 697-714 44 2m1 2 2m 1 GGG ACA TYC GAR TCG A 692-707 45 2a2 2 2a 2 TAC ACT CGC TGA CTG AGA 758-775 46 2b2 2 2b 2 TAC ACT CGC TCA CTG AGA 758-775 47 2c2 2 2c 2 ATA CAC TCA CTG ACT GAG AG 757-776 48 2d2 2 2d 2 CTC ACT GAC TGA GAG GCT 762-779 49 2kc2 2 2k12c 2 ACA CTC ACT NAC TGA GAG ACT 759-779 50 2i2 2 2i 2 TAC ACT CAC TRA CTG AGA GG 758-777 51 2j2 2 2j 2 CAT ACA TTC ACT CAC TGA GA 756-775 52 2l2 2 2l 2 ATY AAA TCA CTG ACA GAG AG 757-776 53 2m2 2 2m 2 ATA CAC TCA YTG ACC GAG A 757-775 54 2a31 2 2a 3 AAA GCY CTA GCG GC 891-905 55 2a32 2 2a 3 CYC TAG CGG CTT GYA 896-910 56 2b31 2 2b 3 AAA GCC CTT GCR GC 892-905 57 2b32 2 2b 3 AAG CCC TCG CRG C 892-905 58 2c3 2 2c 3 AAG CCA GRG CGG C 893-905 59 2d3 2 2d 3 CNR RRG CAG CCT G 896-908 60 2i3 2 2i 3 GCY CAA GCG GCC T 895-907 61 2k3 2 2k 3 AGG CCC TGG CGG 893-904 62 2m3 2 2m 3 AAG CCC AAG GAG CC 893-916 63 3a1 3 3a 1 ACA TCA GGG TGG AAG AG 695-711 64 3b1 3 3b 1 CAT CAG GAC GGA GGA G 696-711 65 3a3 3 3a 3 AAG GCC ACR GCG G 892-904 66 3b3 3 3b 3 AAG GCC ACT GCV GC 894-905 67 3k3 3 3k 3 AAG CAA AGG GAG CC 893-906 68 3a2 3 3a 2 ATC TCC TCC CTC ACG G 757-772 69 3b2 3 3b 2 ATC AGC GCT CTC ACR G 757-772 70 3k2 3 3k 2 TGA TAA CTT GAG TCA CGG 755-772 71 4ac1 4 4a14c 1 AAC CGA AAA GGA CAT CA 684-700 72 4df1 4 4d/4f 1 TRA CYG AAA GAG ACA TCA 683-700 73 4hk1 4 4h14k 1 TGA CTG AAA GGG ACA TCA 683-700 74 4i1 4 4i 1 CGT GAC GGA GAG AGA CA 681-697 75 4n1 4 4n 1 ACT GTG ACT GAG AAA GAC A 679-697 76 4p1 4 4p 1 CCG TGA CTG AGA AGG AC 680-697 77 4r1 4 4r 1 GTC ACC GAA ARR GAC AT 682-692 78 4a21 4 4a 2 GTT ATT GCY GCC CTC A 754-769 79 4dp2 4 4d14p 2 GGT GAT ATC CGC CCT 753-767 80 4a22 4 4a 2 GCA AAG TCA TCA CCG CC 749-765 81 4c2 4 4c 2 ACY GCC CTA ACA GAG AG 760-776 82 4f2 4 4f 2 AGG TRA TAT CCG CCC T 752-767 83 4i2 4 4i 2 AGG TCA TCA AMG CCC 752-766 84 4k2 4 4k 2 ARA CCR ATA TCC GCC CT 751-767 85 4n2 4 4n 2 GYY ATA ACC GCC CTC A 754-769 86 4o2 4 4o 2 CGC CCT TAC RGA GAG 762-776 87 4r2 4 4r 2 AAG GCC ATA ACC GC 751-764 88 4t2 4 4t 2 GGT RAT AYC AGC CCT CA 753-769 89 4a3 4 4a 3 CAA AGC CAC AGC CGC 891-905 90 4c3 4 4c 3 AAA GCC TMA GCC GC 892-905 91 4d3 4 4d 3 TAA GGC CAG CGC AGC 891-905 92 4f3 4 4f 3 YAA GGC YAC MGC GGC 891-905 93 4h3 4 4h 3 ARG CCA CRG CAR CCA 893-907 94 4k3 4 4k 3 TTA AGG CYG YCG CAG 890-904 95 4on3 4 4o/4n 3 AAG ACC ACR GCC GCC 892-907 96 4i3 4 41 3 CCT CAAR GCC ACA GC 891-906 97 4p3 4 4p 3 YAA GGC AAC AGC AGC 891-906 98 4r3 4 4r 3 AAA ACC ACG GCR GCC A 892-907 99 4a4 4 4a 4 TGT GGG TAT CGG AGA TG 820-836 100 4c4 4 4c 4 CGG GTA TCG CAG ATG 822-836 101 4d4 4 4d 4 CGG RAC TCG ACG GTG 822-836 102 4f4 4 4f 4 YGG GTA CCG TAG ATG C 822-837 103 4h4 4 4h 4 CGG GHT TCG GAG GT 822-835 104 4i4 4 4i 4 GTG GCA TCC GTA GAT G 821-836 105 4k4 4 4k 4 GCG GGT ATC GVA GGT G 821-836 106 4o4 4 4o 4 GCC AGC GGA GAT GC 824-837 107 4pt4 4 4p/4t 4 CGG TGT BCG YAG GTG C 822-837 108 4r4 4 4r 4 CGG TTA TCG GAG ATG C 822-837 109 5a 5 5a 1 GYR ATA CGG TCA CTC AC 754-770 110 6a1 6 6a 1 CGG ACT GAG AAC GAC AT 700-716 111 6b1 6 6b 1 CGA ACT GAA GAG GAC ATC 700-717 112 6d1 6 6d 1 CGG ACT GAG GAG GAC AT 700-716 113 6g1 6 6g 1 CGG ACA GAG GAG TCY AT 700-716 114 6h1 6 6h 1 CGC ACA GAA CAA GAC AT 700-716 115 6k1 6 6k 1 ACT GAG CGG GAT GTC T 703-718 116 6a3 6 6a 3 GCA CAG GCC GCC T 895-907 117 6b3 6 6b 3 GCA CAG GCG GCG T 895-906 118 6d3 6 6d 3 AGG CGC AAG CAG C 893-905 119 6g3 6 6g 3 AGG CCA YGG CGG 893-904 120 6h3 6 6h 3 GCA ACC GCC GCT 895-906 * Name of oligonucleotides in accordance with positions thereof in FIG. 3 ** Meaning of the one-letter codes for nucleotides in degenerate oilgonucleotide sequences: R-A, G Y-C, T M-A, C K-G, T S-C, G W-A, T H-A, C, T B-C, G, T V-A, C, G D-A, G, T N-A, C, G, T

Example 2 Reverse Transcription Combined with Polymerase Chain Reaction (RT-PCR) of NS5B Region Fragment; Production of Single-Stranded Fluorescent Labeled Fragment by Asymmetric PCR

First step: reverse transcription combined with the PCR (RT-PCR) to obtain a 418 b.p. NS5B region fragment.

-   A 10 mcl of isolated viral RNA was added to 40 mcl RT-PCR mix (final     volume of 50 mel).

Mix for RT-PCR included:

-   1×RT-PCR buffer: 70 mM Tris-HCl, pH 8.3, 16.6 mM (NH₄)₂SO₄, 7.5 mM     MgCl₂; -   dATP, dCTP, dGTP, dUTP at a concentration 200 !mon each (Sileks,     Russia); -   primers (sequences are presented in Table 2) Pr3_f/Pr2_r at a     concentration of 200 nM each; -   10 units of thermostable ST-polymerase (Sileks, Russia); -   1 unit of uracil-DNA-glycosylase (Sileks, Russia); -   10 units of RNAse inhibitor (Fermentas, Lithuania).

Amplification was carried out on thermocycler PTC-200 Dyad (MJ Research, USA): reverse transcription at 50° C.-30 min, followed by 50 cycles of PCR: 95° C.-30 s, 63° C.-30 s, 72° C.-30 s; final elongation at 72° C.-10 min.

A 1 mcl reaction mix obtained at first step of amplification was used as template for second step.

A second PCR step was carried out in a semi-nested variant with P3_f/Pr5_r primers flanking a 382 b.p. NS5B region. Primer sequences are given in Table 2.

Mix for RT-PCR included (25 mei):

-   1×PCR-buffer: 10 mM KCl, 10 mM Tris-HCl (pH 8.3) (Sileks, Russia); -   1.5 mM MgCl₂; -   dATP, dCTP, dGTP, dUTP at a concentration 200 μmol/L each (Sileks,     Russia); -   fluorescent labeled dUTP at a concentration 10 μmol/L     (“Biochip-IMB”, Russia); -   P3_f/Pr5_r primers at a concentration of 20 nm/100 nM, respectively; -   10 units of thermostable Taq DNA-polymerase (Sileks, Russia).

Amplification was performed on thermocycler PTC-200 Dyad (MJ Research, USA): 95° C.-2 min, then 36 cycles: 95° C.-20s, 60° C.-20 s, 72° C.-30 s, final elognation: 72° C.-5 min. 12 mcl of the obtained product were used in hybridization on a biochip.

TABLE 2 List of primers for the amplification of an NS5B region fragment. Primer position SEQ in NS5B fragment ID sequence NO: Title Sequence 5′→3′* (Acc. No M62321) 121 Pr3_f TATGAYACCCGCTGYTTTGACTC 655-677 122 Pr2_r GGCGGAATTCCTGGTCATAGCCT 1015-1044 CCGTGAA 123 Pr5_r GCTAGTCATAGCCTCCGT 1018-1035 *one-1etter code for nucleotide in degenerate primer sequence: Y = C, T

Example 3 Hybridization of Amplified Labeled Product on Biochip

A 12 mcl reaction mix obtained after a second step of PCR and predominantly comprising DNA single-stranded fluorescent labeled fragments conforming to an NS5B region fragment, as assayed, was added with the concentrated solution of a hybridization buffer such that the final concentration of guanidine thiocyanate was 1 M, HEPES—50 mM, pH 7.5, EDTA—5 mM. The reaction chamber of the biochip was filled with the 32 mcl of resulted hybridization mixture and sealed. Hybridization was performed at 37° C. for 12-18 hours. On completion of hybridization, the biochip was washed thrice with distilled water at 37° C. for 30 s and dried.

Example 4 Registration and Interpretation of Hybridization Results

The registration of fluorescence pattern of biochip was performed using universal fluorescence analyzer (Biochip-IMB, Ltd, Russia) equipped with specialized software ‘ImageWare®’ (Biochip-IMB, Ltd, Russia).

The interpretation of results was performed by the aforesaid algorithm of a software module for the analysis of the fluorescent images of biochips Imageware®.

Example 5 Analysis of NS5B Region of HCV Sample Belonging to Subtype 1a Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 4A shows a biochip hybridization pattern. FIG. 4B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as suggested, analysis starts off with computing a mean signal (I_(ref)) in empty elements, in which particular case the I_(ref) is 0.62. In accordance with this value and the threshold value of 1.5, the signals are filtered into genotype and subtype-specific elements, with the result that the signals in group G1 containing genotype 1-specific probes exceed the I_(ref) 1.5 times or more. A similar situation is evolved around the signal in a element G4-2 (1.37). The signals in other groups containing genotype-specific probes were close to background ones. Furthermore, the maximum signal is detected from group G1, G1-2 (5.7). The signal in the given element exceeds a signal G4-2 more than 1.5 times. So the sequence of the analyzed HCV sample, as assayed, relates to a genotype 1.

An analysis in the groups of elements comprising subtype-specific probes belonging to genotype 1 goes to show: In group I, the maximum (exceeding a 1.5 threshold value with respect to the remaining elements) signals have 1a11 (17.0) and 1a12 (17.0). In group 2-1a2 (16.4). In group 3-1a32 (3.4). In group 4-1a4 (3.1). Thus, in all the groups, a maximum signal is characteristic of the elements comprising the probes specific for subtype 1a. This means, that the analyzed HCV specimen is related to the subtype 1a.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 1a sequences.

Thus, it has been established that an HCV RNA specimen, as assayed, has a genotype 1 and a subtype 1a, which coincides with sequencing results in full.

Example 6 Analysis of NS5B Region of HCV Sample Belonging to Subtype 1b Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 5A shows a biochip hybridization pattern. FIG. 5B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as suggested, analysis starts off with computing a mean signal (I_(ref)) in empty elements, in which particular case the I_(ref) is 0.67. In accordance with this value and the threshold value of 1.5, the signals are filtered in genotype-and subtype—specific elements. The result is that the signals in G1 group containing genotype 1—specific probes exceed the I_(ref) 1.5 times or more (the maximum signal is characteristic of a G1-3 element (5.69)). The signals in other groups containing the genotype-specific probes were close to background ones. So the sequence of the analyzed HCV sample, as assayed, relates to a genotype 1.

Analysis in the groups of elements containing subtype-specific probes of genotype 1 subtypes reveals the following: in group 1, the maximum (i.e. exceeding a threshold value 1.5 times vs other elements) signal has 1 bd1 (18.0). In group 2-1b2 (16.3). In group 4-1b4 (3.9). In group 1 a perfect duplex with a DNA, as assayed, forms also an oligonucleotide whose sequence is universal for subtypes 1b and 1d. However, the maximum signal is registered also in the elements containing probes specific only for the subtype 1b-1b2. and 1b4. Consequently, the assayed specimen relates to the subtype 1b.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 1b sequences.

Thus, it has been established that an HCV RNA specimen, as assayed, has a genotype 1 and a subtype lb which fully coincides with sequencing results.

Example 7 Analysis of NS5B Region of HCV Sample Belonging to Subtype 1e Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 6A shows a biochip hybridization pattern. FIG. 6B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal NO in empty elements. Here the value of I_(ref) is 0.39. According to this value and the threshold value of 1.5, the signals are filtered in genotype-and subtype-specific elements. The result: the signals in group G1 comprising probes showing specificity to a genotype 1 exceed the I_(ref) 1.5 times or more. The signals in other groups of elements containing the genotype-specific probes were close to background ones. The maximum signal in the group G1 is characteristic of a G1-3 element (4.82). So the sequence of the analyzed HCV sample relates to a genotype 1.

Analysis in the groups of elements containing probes specific for genotype 1 subtypes goes to show: in group I, the maximum (exceeding the threshold value of 1.5 with respect to other elements) signal has 1cel (18.0). In group 2-1e2 (8.46). In group 3-1e3 (3.52). In group 4-1e4 (2.18). The perfect duplex with target hybridized NS5B fragment in group 1 was formed by the oligonucleotide with the sequence matching the subtypes 1c and 1e. However, the maximum signal is also registered in elements containing probes specific only for subtypes 1e -1e2, 1e3 and 1e4. If follows that the specimen, as assayed, is related to the subtype 1e.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 1e sequences.

Thus, it has been established that an HCV RNA specimen as assayed has a genotype I and a subtype 1e, which fully coincides with sequencing results.

Example 8 Analysis of NS5B Region of HCV Sample Belonging to Subtype 2a Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 7A shows a biochip hybridization pattern. FIG. 7B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal (I_(ref)) in empty elements. In this case, the value of I_(ref) is 0.25. According to this value and the 1.5 threshold value, filtration of the signals is carried out in genotype- and subtype-specific elements. As a result, the signals in group 2 elements comprising probes showing specificity to a genotype 2 exceed the I_(ref) 1.5 times or more. The signal in a G6 element (2.01) is likewise valid relative to the I_(ref). The maximum signal in the group 2 is characteristic of an element G2-2 (15.6) exceeding the signal in a G6 element more than 1.5 times. It follows that the sequence of the analyzed HCV sample relates to a genotype 2.

Assaying in the groups of elements comprising the subtype-specific probes of genotype 2 has revealed: in group 1 the maximum (i.e. exceeding a 1.5 threshold value in relation to other elements) signal has 2ad1 (15.2). In group 2-2a2 (6.62). In group 3-2a31 (2.33). In all three groups, the maximum signal is characteristic of the elements containing probes specific for a subtype 2a. So, the specimen as assayed refers to the subtype 2a.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 2a sequences.

It is hence only logical to deduce that an HCV RNA specimen as assayed has a genotype 2 and a subtype 2a, which fully coincides with sequencing results.

Example 9 Analysis of NS5B Region of HCV Sample Belonging to Subtype 2i Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 8A shows a biochip hybridization pattern. FIG. 8B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal (I_(ref)) in empty elements. In this case, the value of I_(ref) is 0.44. In accordance with this value and a 1.5 threshold value, the signals are filtered in genotype- and subtype-specific elements with the result that only the signals in elements of group G2 with genotype 2-specific probes exceed the I_(ref) 1.5 times or more. The maximum signal in the group G2 is characteristic of an element C2-3 (15.9). It follows that the sequence of the analyzed HCV sample relates to a genotype 2.

Assaying in the groups of elements comprising the subtype-specific probes of genotype 2 has revealed: in group I, the maximum (i.e. exceeding a 1.5 threshold value relative to other elements) signal has 2i1 (2.3). In group 2-2kc2 (10.9). In group 3-2i3 (4.31). In group 2, the perfect duplexes are provided with an assayed DNA with an oligonucleotide whose sequence is universal for subtypes 2c and 2k. However, in two other groups, the maximum signal belongs to the elements containing unique oligonucleotides showing a specificity to a subtype 2i. In accordance with the presently claimed algorithm of interpretation, the specimen as assayed refers to the subtype 2i.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 2i sequences.

Thus, it has been ascertained that an HCV RNA specimen as assayed has a genotype 2 and a subtype 2i, which fully coincides with sequencing results.

Example 10 Analysis of NS5B Region of HCV Sample Belonging to Subtype 3a Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 9A shows a biochip hybridization pattern. FIG. 9B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal (I_(ref)) in empty elements. In this case, the value of I_(ref) is 0.52. According to this value and a 1.5 threshold value, the signals are filtered in genotype- and subtype-specific elements. As a result, the signals in group G3 containing probes specific for a genotype 3 exceed the I_(ref) 1.5 times or more. The signal in a G4-2 element (0.85) likewise exceeds the I_(ref) 1.5 times. The signals in other groups of elements containing genotype-specific probes are close to background ones. The maximum signal in the group G3 is characteristic of a G3-1 element (15.4) whose signal exceeds that of G4-2 more than 1.5 times. It follows that the sequence of the analyzed HCV sample relates to a genotype 3.

Assaying in the groups of elements containing subtype-specific probes of genotype 3 reveals the following: in group I the maximum (i.e. exceeding a 1.5 threshold value relative to other elements) signal is characteristic of a 3a1 element (16.2). In group 2-3a2 (4.69). In group 3-3a3 (1.74). And, as so, in all the groups, the maximum signal is featured by probe-containing elements showing a specificity to a subtype 3a. Consequently the specimen as assayed is related to the subtype 3a.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 3a sequences.

Thus, it has been established that an HCV RNA specimen as assayed has a genotype 3 and a subtype 3a, which is in full coincidence with sequencing results.

Example 11 Analysis of NS5B Region of HCV Sample Belonging to Subtype 4a Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 10A shows a biochip hybridization pattern. FIG. 10B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal (I_(ref)) in empty elements. In this case, the value of I_(ref) is 0.55. In accordance with this value and a 1.5 threshold value, the signals are filtered in genotype-and subtype-specific elements. As a result, only the signals in G4 group elements containing probes specific for a genotype 4 exceed the I_(ref) 1.5 times or more. The signals in the remaining elements containing genotype-specific oligonucleotides were close to background ones. The maximum signal in the G4 group is registered in a G4-3 element (17.9). It follows that the RNA sequence of a specimen as assayed is related to the genotype 4.

Assaying in groups containing subtype-specific probes of genotype 4 reveals the following points: in three groups of probes specific for a genotype 4, the maximum signals belong to the elements containing probes for detecting a subtype 4a: 4ac1 (16.3), 4a21 (1.08), 4a4 (14.1). In group 3, the maximum signal belongs to a 4on3 element (1.21); however, in accordance with the algorithm, as shown and described, the specimen as assayed refers to the subtype 4a.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 4a sequences.

With that so, it has been established that an HCV RNA specimen as assayed has a genotype 4 and a subtype 4a, which is in full coincidence with sequencing results.

Example 12 Analysis of NS5B Region of HCV Sample Belonging to Subtype 4d Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 11A shows a biochip hybridization pattern. FIG. 11B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal (I_(ref)) in empty elements. In this case, the value of I_(ref) is 0.35. According to this value and a 1.5 threshold value, the signals are filtered in genotype- and subtype-specific elements. As a result, the signals in G4 group elements containing probes specific for a genotype 4 exceed the I_(ref) 1.5 times or more. The signals in the rest of elements containing genotype-specific oligonucleotides were close to background ones. The maximum signal in the G4 group belongs to a G4-1 element (17.4). It follows that the RNA sequence of a specimen as assayed is related to the genotype 4.

Assaying in the groups of subtype-specific probes of genotype 4 reveals the following points: in group I, the maximum signal is featured by a 4df1 element, (1.1.6) in group 2-4dp2 element (3.16), in group 3-4d3 element (1.95), in group 4-4d4 (7.35). In all groups, the maximum signal is characteristic of probe-containing elements specific for a subtype 4d. Consequently a specimen as assayed is related to the subtype 4d.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 4d sequences.

Thus, it has been established that an HCV RNA specimen as assayed has a genotype 4 and a subtype 4d, which fully coincides with sequencing results.

Example 13 Analysis of NS5B Region of HCV Sample Belonging to Subtype 5a Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 12A shows a biochip hybridization pattern. FIG. 12B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal NO in empty elements. In this case, the value of I_(ref) is 0.28. According to this value and a 1.5 threshold value, the signals are filtered in genotype- and subtype-specific elements, with the result that only the signals in group G5 elements containing probes specific for a genotype 5 exceed the I_(ref) 1.5 times or more. The maximum signal in the G5 group is characteristic of a G5-1 element (6.58). It follows that the RNA sequence of a specimen as assayed is related to the genotype 5. Inasmuch as the latter has only one subtype, 5a, and the signal in a 5a2 element showing a specificity to the given subtype is actual, a conclusion might be drawn that the specimen as assayed has the subtype 5a.

A sequencing method with subsequent phylogenetic analysis showed that the sequence being assayed falls within a cluster of subtype 5a sequences

Thus, it has been established that an HCV RNA specimen as assayed has a genotype 5 and a subtype 5a, which is in full coincidence with sequencing results.

Example 14 Analysis of NS5B Region of HCV Sample Belonging to Genotype 6 Using Hybridization on Biochip

An HCV viral RNA was isolated from patient's blood specimen using Qiamp Viral RNA mini kit (Qiagen, Germany) under the protocol of manufacturer. The isolated RNA was used in RT-PCR as described (Example 2). The presence of an amplified NS5B 418 b.p. long fragment was tested by electrophoresis in agarose gel whereupon a RT-PCR product was divided into two portions of which one was treated and assayed according to the methods as described in Examples 2-4 (a second PCR step followed by hybridization on a biochip, washing, registration and interpretation of the fluorescent pattern of the biochip). The second portion of a first step product was used upon additional purification in sequencing reaction, followed by analysis on an automatic sequencer, correcting a chromatogram and obtaining the sequence of NS5B region fragment, constructing a multiple alignment and a phylogenetic tree on whose basis a genotype and a subtype were determined.

FIG. 13A shows a biochip hybridization pattern. FIG. 13B demonstrates the distribution of the normalized fluorescence signals of biochip elements.

In accordance with the algorithm of results interpretation, as proposed, analysis begins with the computation of a mean signal (I_(ref)) in empty elements. In this case, the value of I_(ref)is 0.72. According to this value and a 1.5 threshold value, signals are filtered in genotype—and subtype-specific elements. As a result, the signals in group G6 element (18.6) comprising a probe showing a specificity to a genotype 6 exceed the I_(ref) 1.5 times or more. The signal in a G3-1 element (5.2) is also to be considered valid; The G6 element exceeds the signal in the G3-1 element more than 1.5 times, which means the identity of analyzed HCV specimen to the genotype 6.

Out of two groups containing probes specific for genotype 6 subtypes, the signal in none of the elements reaches a threshold value relative to I_(ref). It follows that in the given specimen an HCV subtype is undetermined and is classified as 6×.

A sequencing method with subsequent phylogenetic assay goes to show that the sequence, as assayed, falls within none on the clusters of genotype 6 subtypes and forms a separate branch of a phylogenetic tree, or—to be more exact—it is unclassified. It is hence only logical to see that the results obtained in both methods confirm the impossibility to clearly define the subtype of the given specimen.

Thus, the invention as submitted permits identifying the genotype and subtype of Hepatitis C virus, on the basis of the analysis of an NS5B region using a biological microchip. A method permits identifying all HCV 6 genotypes and 36 subtypes, with the most virulent and drug resistant forms included. The method of the present invention advantageously differs from the existing analogs in high specificity as to the identification of genotype 1 subtypes, more exactly, a lb subtype, and also in simplicity of execution and low cost. Data obtained through the use of a method of hybridization on biochips of the invention, as being claimed and as set forth in the application, can be used for estimation and prognosis of disease severity (acute/chronic cirrhosis, a likelihood of development of liver cancer), determining a therapeutic dosage of medicaments and duration of a course of therapy as well as for epidemiologic genotyping.

All patents, publications, scientific articles and other documents and materials, as referenced or mentioned herein are hereby incorporated by reference to the same extent as if each of these documents had been incorporated by reference in its entirety individually or set forth herein in its entirety.

Although the preferred embodiments of the present invention and their advantages are shown and described above in greater detail, a person skilled in the art will be in a position to make changes and modifications without departing from the spirit and scope of the present invention as defined by the appended claims. 

1. A method of identifying a genotype and a subtype of hepatitis C virus, on the basis of the analysis of an HCV genome NS5B region, comprising: (a)—reverse transcription combined with PCR (RT-PCR) using a virus RNA as a template and a first pair of primers showing a specificity to an NS5B region fragment; (b)—asymmetric amplification of the NS5B region fragment using as template a RT-PCR product obtained in (a), a second pair of specific primers and a mixture of four deoxynucleoside triphosphates wherein one of the four deoxynucleoside triphosphates is fluorescent labeled, as a substrate, to provide substantially a single-stranded fluorescent labeled fragment; (c)—providing a biochip for the identification of the HCV genotype and subtype that represents a support comprising a set of discrete elements, with a unique oligonucleotide probe immobilized in each of them, having a sequence complementary to the sequence of a single-stranded fragment obtained in step (b) and selected from the group comprising: a) the NS5B region fragment sequences specific for each of the HCV genotypes (genotype-specific); and b) NS5B region fragment sequences specific for each of the HCV subtypes (subtype-specific); (d)—hybridization of the amplified labeled product provided in step (b) on a biochip with the formation of duplexes with immobilized probes in conditions providing for a single-nucleotide resolution between the perfect and imperfect duplexes; (e)—registration and interpretation of hybridization results.
 2. The method of claim 1, wherein in step (a) a first pair of specific primers is used whose sequences are set forth in SEQ ID NO: 121 and
 122. 3. The method of claim 1, wherein in step (b) a second pair of specific primers is used whose sequences are set forth in SEQ ID NO: 121 and
 123. 4. The method of claim 1, wherein in step (b) one of the primers of the second pair is used in an at least tenfold molar excess relative to the second primer.
 5. The method of claim 1, wherein in step (b), the fluorescent labeled deoxynucleoside triphosphate used corresponds to the fluorescent labeled deoxyuridine triphosphate.
 6. The method of claim 1, wherein the biochip is a biochip based on hydrogel elements that is obtained by a procedure of chemically or photoinduced copolymerization.
 7. The method of claim 1, wherein the biochip comprises a set of immobilized oligonucleotides whose sequences are defined in SEQ ID NO: 1-120.
 8. The method of claim 1, wherein registration of the results in step (e) is performed through the use of a portable analyzer of fluorescence and software, which permits using the software-based processing of signal intensities with the subsequent interpretation of results.
 9. The method of claim 1, wherein the interpretation of registered results in step (e) is performed in two steps: 1) assaying the signals in biochip elements comprising oligonucleotide probes specific for HCV genotypes thereby to identify the genotype of a specimen as assayed; 2) in the event of identification of a genotype, assayed are only biochip elements containing oligonucleotide probes specific for the subtypes of an identifiable genotype, regardless of presence of the signals in the elements containing the probes specific for the subtypes of other genotypes.
 10. The method of claim 1 further comprising evaluating and predicting severity of a disease (acute/chronic cirrhosis, the likelihood of development of liver cancer), determining a therapeutic dosage of medicaments and a course of therapy and/or epidemiological genotyping on the basis of interpretation of hybridization results.
 11. A biochip for identifying an HCV genotype and subtype, on the basis of the analysis of NS5B region that represents a support containing a set of discrete elements, with a unique oligonucleotide probe immobilized in each of them and what is more probe sequences are defined in SEQ ID NO: 1-120.
 12. The biochip of claim 12, wherein it is a biochip based on hydrogel elements that is obtained by a procedure of chemically or photoinduced copolymerization.
 13. A set of oligonucleotide probes for producing a biochip for the identification of an HCV genotype and subtype, on the basis of the analysis of an NS5B region whose sequences are defined in SEQ ID NO: 1-120.
 14. A method for designing a set of oligonucleotide probes usable for the construction of a biochip for the identification of a HCV genotype and subtype, on the basis of the analysis of an NS5B region providing for the separate selection of several discriminating probes for each and every genotype and subtype whose sequences are complementary to the sequences of different segments of an NS5B region fragment as assayed. 